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BPS4104/BIO8102H Bioinformatics (Winter term)

Course description:

The rapid development of molecular biology and biotechnology has resulted in rapid accumulation of genomic, transcriptomic and proteomic data. These data, centralized in major databases and databanks, is equivalent to ever-expanding oceans with enormous fish and whale stocks waiting to be harvested. Bioinformatics, an interdisciplinary science founded by the joint effort of biologists, computer scientists, mathematicians and statisticians, studies the oceans of data and design efficient fishing fleet to harvest the resources.

This course will show you the ocean and put you on the fishing fleet. Practical application of quantitative and computational methods to solve biological problems will be illustrated to enhance understanding.

Learning outcomes:

  1. To gain skills and experience in applying scientific methods to problem-solving, e.g., how to formulate hypotheses, derive predictions and test these predictions.
  2. To acquire practical experience in using bioinformatic tools to discover and characterize sequence motifs, and how the interaction between sequence motifs and their decoders affect molecular processes such as genome replication, transcription, RNA processing, and translation in viruses, prokaryotes and eukaryotes
  3. To understand bioinformatic algorithms as building blocks to build new bioinformatic tools for new research problems.
  4. To relate bioinformatic tools to human diseases and drug development.
  5. To develop skills in scientific communication.

Textbook

Xia, X. 2018. Bioinformatics and the cell: Modern computational approaches in genomics, proteomics and transcriptomics (2nd edition. You can download the book free or purchase a hard copy for $24.99.

Lab manual

Download as a PDF file.

Web page:

bps4104.aspx

Teaching methods:

Lectures and computer laboratories

Attendance:

As per uOttawa policy, to ensure they succeed in all courses of their program of study, students have the responsibility to participate in the various learning and assessment activities for this course.

Instructor:

Prof. Xuhua Xia, Rm. 278, 30 Marie Curie.
E-mail: xxia@uottawa.ca
Phone: 562-5800 ext 6886
Office hour: Email me any time. I will reply directly to you or to the class if relevant.

Teaching assistants:

Yulong Wei: ywei025@uottawa.ca
Alibek Kruglikov: akrug104@uottawa.ca

Evaluation:

Evaluation methods and weights:

  • Timed take-home mid-term exam #1 (1.5 hr, done during lab session): 20%
  • Timed take-home mid-term exam #2 (1.5 hr, done during lab session): 20%
  • Laboratory reports every week: 30%
  • Timed take-home exam (3 hr): 30%

Notes:

  • If we have 11 labs and you submitted only 2 lab reports, then your average final lab mark will NOT be the average of the two, but will be (Mark1+Mark2)/11. However, if sickness (or some equally valid reasons) prevents you from submitting 3 lab reports, please let TA know and your final lab mark will be (Mark1+Mark2)/(11-3).
  • Late assignments will be penalized 20% per day unless you provide TA with reasons.
  • Marking disputes: If you feel an error has been made in the grading of an assignment or exam, you have 10 working days from the date the item was returned to request a regrading. Beyond 10 working days the mark is considered final. If the issue concerns an assignment, please consult the TA that marked it (see above); if it concerns an exam, please email me.
  • When a regrading occurs, the new mark will stand whether it is higher or lower, so there is no guarantee your mark will increase. Simple adding mistakes unfortunately happen on occasion given the volume of assignments and exams we have to mark and such cases are easy to correct. However, disputes over partial marks on partially correct answers will not always work out in your favour and should be reserved for cases in which you feel you have a strong justification. When requesting a regrading, you must provide an explanation as to what you feel the issue is (i.e. why you think you deserve a higher grade). The more specific this is the better your chance of success.
  • Exams are cumulative. Students who miss an exam due to medical reasons (a doctor's note is needed) will take a deferred exam (0 mark if no medical reason is given).

Plagiarism

Plagiarism is the act of passing off someone else's words or ideas as your own. Plagiarism is a major academic offence (see the University of Ottawa regulation on academic fraud) and is also illegal. We uphold the law. It is critical that you understand what constitutes plagiarism and how you can avoid it. For more information, consult the Student's Guide on Academic Integrity from the Student Academic Success Service.

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